tbuckley/cabot-search huggingface dataset:
UK and Ireland Joint Advisory Group (JAG) consensus statements for training and certification in diagnostic endoscopic ultrasound (EUS)
Authors: Tareq El Menabawey, Raymond McCrudden, Dushyant Shetty, Andrew D Hopper, Matthew T Huggett, Noor Bekkali, Nicholas R Carroll, Elaine Henry, Gavin J Johnson, Margaret G Keane, Mark Love, Colin J McKay, Sally Norton, Kofi Oppong, Ian Penman, Jayapal Ramesh, Barbara Ryan, Keith Siau, Manu Nayar
Journal: Gut (2023)

Background and aims International endoscopy societies vary in their approach for credentialing individuals in endoscopic ultrasound (EUS) to enable independent practice; however, there is no consensus in this or its implementation. In 2019, the Joint Advisory Group on GI Endoscopy (JAG) commissioned a working group to examine the evidence relating to this process for EUS. The aim of this was to develop evidence-based recommendations for EUS training and certification in the UK. Methods Under the oversight of the JAG quality assurance team, a modified Delphi process was conducted which included major stakeholders from the UK and Ireland. A formal literature review was made, initial questions for study were proposed and recommendations for training and certification in EUS were formulated after a rigorous assessment using the Grading of Recommendation Assessment, Development and Evaluation tool and subjected to electronic voting to identify accepted statements. These were peer reviewed by JAG and relevant stakeholder societies before consensus on the final EUS certification pathway was achieved. Results 39 initial questions were proposed of which 33 were deemed worthy of assessment and finally formed the key recommendations. The statements covered four key domains, such as: definition of competence (13 statements), acquisition of competence (10), assessment of competence (5) and postcertification mentorship (5). Key recommendations include: (1) minimum of 250 hands-on cases before an assessment for competency can be made, (2) attendance at the JAG basic EUS course, (3) completing a minimum of one formative direct observation of procedural skills (DOPS) every 10 cases to allow the learning curve in EUS training to be adequately studied, (4) competent performance in summative DOPS assessments and (5) a period of mentorship over a 12-month period is recommended as minimum to support and mentor new service providers. Conclusions An evidence-based certification pathway has been commissioned by JAG to support and quality assure EUS training. This will form the basis to improve quality of training and safety standards in EUS in the UK and Ireland.
Shorter-acting glucagon-like peptide-1 receptor agonists are associated with increased development of gastro-oesophageal reflux disease and its complications in patients with type 2 diabetes mellitus: a population-level retrospective matched cohort study
Authors: Benjamin Douglas Liu, Sharon C Udemba, Katherine Liang, Yasir Tarabichi, Hannah Hill, Ronnie Fass, Gengqing Song
Journal: Gut (2023)

Shorter half-life glucagon-like peptide-1 receptor agonists (GLP-1 RAs) delay gastric emptying (DGE) more than GLP-1 RAs with longer half-lives. DGE is a known risk factor for gastro-oesophageal reflux disease (GERD) and its complications.
Development and Current State of Digital Therapeutics for Irritable Bowel Syndrome
Authors: Darren M. Brenner, Amy M. Ladewski, Sarah Wimberly Kinsinger
Journal: Clinical Gastroenterology and Hepatology (2023)

Irritable bowel syndrome (IBS) is a common, debilitating disorder characterized by abdominal pain and disordered bowel habits. Current pharmacologic treatments often provide incomplete symptom relief and may be poorly tolerated. Furthermore, alleviation of gastrointestinal symptoms does not always translate into improved quality of life for IBS patients. Current treatment guidelines recommend brain-gut behavior therapy (BGBT) in conjunction with other IBS therapies, and, in randomized controlled trials, BGBT has been shown to improve symptoms, patient satisfaction, functioning, and quality of life. Access to BGBT is limited by lack of adequately trained gastrointestinal psychologists, patient time constraints, and cost. Furthermore, clinician knowledge that BGBT is specific, and different from psychotherapy approaches for common mental health disorders, may limit referrals even where available. This review provides an overview of the pathophysiology of IBS, disease burden, unmet therapeutic needs, evidence base of novel digital therapeutics for IBS, and guidance on the introduction and appropriateness of these interventions for patients.
Machine learning-based integration develops a metabolism-derived consensus model for improving immunotherapy in pancreatic cancer
Authors: Yongdong Guo, Ronglin Wang, Jingjie Shi, Cheng Yang, Peixiang Ma, Jie Min, Ting Zhao, Lei Hua, Yang Song, Junqiang Li, Haichuan Su
Journal: Journal for ImmunoTherapy of Cancer (2023)

Pancreatic cancer (PAC) is one of the most malignant cancer types and immunotherapy has emerged as a promising treatment option. PAC cells undergo metabolic reprogramming, which is thought to modulate the tumor microenvironment (TME) and affect immunotherapy outcomes. However, the metabolic landscape of PAC and its association with the TME remains largely unexplored. We characterized the metabolic landscape of PAC based on 112 metabolic pathways and constructed a novel metabolism-related signature (MBS) using data from 1,188 patients with PAC. We evaluated the predictive performance of MBS for immunotherapy outcomes in 11 immunotherapy cohorts from both bulk-RNA and single-cell perspectives. We validated our results using immunohistochemistry, western blotting, colony-formation assays, and an in-house cohort. MBS was found to be negatively associated with antitumor immunity, while positively correlated with cancer stemness, intratumoral heterogeneity, and immune resistant pathways. Notably, MBS outperformed other acknowledged signatures for predicting immunotherapy response in multiple immunotherapy cohorts. Additionally, MBS was a powerful and robust biomarker for predicting prognosis compared with 66 published signatures. Further, we identified dasatinib and epothilone B as potential therapeutic options for MBS-high patients, which were validated through experiments. Our study provides insights into the mechanisms of immunotherapy resistance in PAC and introduces MBS as a robust metabolism-based indicator for predicting response to immunotherapy and prognosis in patients with PAC. These findings have significant implications for the development of personalized treatment strategies in patients with PAC and highlight the importance of considering metabolic pathways and immune infiltration in TME regulation.
Taking a collateral history: the missing piece of the puzzle
Authors: Kyra Neubauer, Heather Brant, Clare Thomas, Sarah Biggs, Elizabeth Hill, Sabi Redwood
Journal: BMJ (2023)

### What you need to know When someone is unable to give a full, detailed, or accurate account of their medical, functional, or social situation, the relevant information may be gathered from others, such as family, friends, or carers. This is known as the collateral history. In this overview, we highlight the benefits and challenges of collecting an effective collateral history and suggest ways to improve collateral history taking. Collateral histories are used to make diagnoses and formulate ongoing medical and social management plans (box 1). There are clinical conditions where collateral histories are commonly needed and often are the sole information source about the patient. These may include patients presenting with epilepsy, syncope, delirium, dementia,12 psychiatric disorders,34 and frailty. Collateral histories can also enhance or verify the narrative given by a patient and may be helpful, or pivotal, for any patient’s care (box 2). Box 1 ### What is a collateral history?RETURN TO TEXT
G20 summit in India: unveiling the digital health initiative with ‘Vasudhaiva Kutumbakam’
Authors: Hitesh Chopra, None Priyanka, Om Prakash Choudhary, Talha B. Emran
Journal: International Journal of Surgery (2023)

Chopra, Hitesh PhD; Priyanka, PhD; Choudhary, Om Prakash PhD; Bin Emran, Talha PhD Author Information
Interplay between diet, circulating indolepropionate concentrations and cardiometabolic health in US populations
Authors: Yang Hu, Jun Li, Biqi Wang, Lu Zhu, Yanping Li, Kerry L Ivey, Kyu Ha Lee, A Heather Eliassen, Andrew Chan, Curtis Huttenhower, Frank B Hu, Qibin Qi, Eric B Rimm, Qi Sun
Journal: Gut (2023)

Objectives To identify indolepropionate (IPA)-predicting gut microbiota species, investigate potential diet–microbiota interactions, and examine the prospective associations of circulating IPA concentrations with type 2 diabetes (T2D) and coronary heart disease (CHD) risk in free-living individuals. Design We included 287 men from the Men’s Lifestyle Validation Study, a substudy of the Health Professionals Follow-Up Study (HPFS), who provided up to two pairs of faecal samples and two blood samples. Diet was assessed using 7-day diet records. Associations between plasma concentrations of tryptophan metabolites and T2D CHD risk were examined in 13 032 participants from Nurses’ Health Study (NHS), NHSII and HPFS. Results We identified 17 microbial species whose abundance was significantly associated with plasma IPA concentrations. A significant association between higher tryptophan intake and higher IPA concentrations was only observed among men who had higher fibre intake and a higher microbial species score consisting of the 17 species (p-interaction&lt;0.01). Dietary and plasma concentrations of tryptophan and most kynurenine pathway metabolites were positively associated with T2D risk (HR Q5 vs Q1 ranged from 1.17 to 1.46) while a significant inverse association was found for IPA (HR Q5 vs Q1 (95% CI) 0.70 (0.56 to 0.88)). No associations were found in CHD for any plasma tryptophan metabolites. Conclusions Specific microbial species and dietary fibre jointly predicted significantly higher circulating IPA concentrations at higher tryptophan intake. Dietary and plasma tryptophan, as well as its kynurenine pathway metabolites, demonstrated divergent associations from those for IPA, which was significantly predictive of lower risk of T2D.
Exploring the impact of gut microbial metabolites on inactivated SARS-CoV-2 vaccine efficacy during pregnancy and mother-to-infant antibody transfer
Authors: Xi Fu, Bingqian Du, Pei-An Chen, Aga Shama, Baolan Chen, Xi Zhang, Xue Han, Yingxia Xu, Yajie Gong, Xia Zeng, Chongzhen Sun, Wenhan Yang, Xiaohui Xing, Zhongjun Li, Yanyan Fu, Dongyun Ke, Niping Wang, Yun Xia, Yu Sun, Qingsong Chen
Journal: Gut (2023)
A Rare Case of Esophageal Granular Cell Tumor in Eosinophilic Esophagitis
Authors: Yousaf Abughofah, Grace E. Kim, Dennis Chen
Journal: Clinical Gastroenterology and Hepatology (2023)

A 25-year-old man with recently diagnosed eosinophilic esophagitis presented for a surveillance esophagogastroduodenoscopy (EGD). He was incidentally found to have a 2-mm submucosal-appearing nodule with a yellow hue in the distal esophagus (Figure A, arrow). The patient denied unintentional weight loss; gastrointestinal symptoms; family history of gastrointestinal malignancy; or tobacco, alcohol, or drug history. Initial biopsies of the lesion showed normal pathology; repeat EGD with stacked biopsies showed granular cell tumor (GCT; Figure B, star) and endoscopic ultrasound showed no deep tumor invasion. The patient was referred for resection and underwent en bloc band-assisted endoscopic mucosal resection (Figures C and D) with pathology confirming GCT without additional abnormalities. Patient is currently asymptomatic and pending surveillance EGD. GCTs are a rare and usually benign neoplasm most often found in the skin and soft tissue, most commonly presenting in females between the 4th and 6th decades of life. They originate from Schwann cells and have been hypothesized to be related to tissue injury or inflammation. Because of its rarity, the true incidence of GCTs is unclear; however, esophageal GCTs are rising in incidence. Esophageal GCTs are typically subepithelial and characterized by a yellow or white appearance as described in this case report. Their clinical course is rather indolent; previous studies of patients undergoing conservative surveillance for GCTs show stability of tumor sizes up to 5 years after initial diagnosis. Rarely, malignant forms of GCTs have been described, with older age and tumor size greater than 5 cm associated with increased malignant risk. Gastrointestinal involvement of GCT only comprises 8% of all GCTs, and this case highlights a unique coexistence of esophageal GCT in the setting of eosinophilic esophagitis, a chronic inflammatory disease. More research is needed to examine the possible role of eosinophilic inflammation in the pathogenesis of GCTs. The authors thank Pari Jafari, MD, for providing the pathology slide.
Beware of drug resistance: Let’s not lose tecovirimat against mpox
Authors: Christophe Van Dijck, Ian Crozier, Koen Vercauteren, Isabel Brosius, Placide Mbala-Kingebeni, Lori Dodd, Emmanuel Bottieau, Olivier Tshiani Mbaya, Veronique Nussenblatt, Johan Neyts, Laurens Liesenborghs
Journal: Clinical Microbiology and Infection (2023)
Effectiveness and safety of tuberculosis preventive treatment for contacts of patients with multidrug-resistant tuberculosis: a systematic review and meta-analysis
Authors: Guozhong Zhou, Shiqi Luo, Jian He, Nan Chen, Yu Zhang, Shunli Cai, Xin Guo, Hongbo Chen, Chao Song
Journal: Clinical Microbiology and Infection (2023)

Contacts of patients with multidrug-resistant tuberculosis (MDR-TB) are at risk of developing TB disease. Tuberculosis preventive treatment (TPT) is an intervention that can potentially reduce this risk.
KLRG1 expression on natural killer cells is associated with HIV persistence, and its targeting promotes the reduction of the viral reservoir
Authors: Antonio Astorga-Gamaza, David Perea, Nerea Sanchez-Gaona, Marta Calvet-Mirabent, Ana Gallego-Cortés, Judith Grau-Expósito, Ildefonso Sanchez-Cerrillo, Joan Rey, Josep Castellví, Adrian Curran, Joaquin Burgos, Jordi Navarro, Paula Suanzes, Vicenç Falcó, Meritxell Genescà, Enrique Martín-Gayo, Maria J. Buzon
Journal: Cell Reports Medicine (2023)

Human immunodeficiency virus (HIV) infection induces immunological dysfunction, which limits the elimination of HIV-infected cells during treated infection. Identifying and targeting dysfunctional immune cells might help accelerate the purging of the persistent viral reservoir. Here, we show that chronic HIV infection increases natural killer (NK) cell populations expressing the negative immune regulator KLRG1, both in peripheral blood and lymph nodes. Antiretroviral treatment (ART) does not reestablish these functionally impaired NK populations, and the expression of KLRG1 correlates with active HIV transcription. Targeting KLRG1 with specific antibodies significantly restores the capacity of NK cells to kill HIV-infected cells, reactivates latent HIV present in CD4+ T cells co-expressing KLRG1, and reduces the intact HIV genomes in samples from ART-treated individuals. Our data support the potential use of immunotherapy against the KLRG1 receptor to impact the viral reservoir during HIV persistence.
Functional architecture of dopamine neurons driving fear extinction learning
Authors: Ximena I. Salinas-Hernández, Daphne Zafiri, Torfi Sigurdsson, Sevil Duvarci
Journal: Neuron (2023)

The ability to extinguish fear responses to stimuli that no longer predict danger is critical for adaptive behavior and increases the likelihood of survival. During fear extinction, dopamine (DA) neurons signal the absence of the expected aversive outcome, and this extinction prediction error (EPE) signal is crucial for initiating and driving extinction learning. However, the neural circuits underlying the EPE signal have remained elusive. Here, we investigate the input-output circuitry of EPE-encoding DA neurons in male mice. By employing projection-specific fiber photometry and optogenetics, we demonstrate that these neurons project to a restricted subregion of the nucleus accumbens. Comprehensive anatomical analyses, as well as projection-specific chemogenetic manipulations combined with recordings of DA biosensors, further uncover the dorsal raphe as one key input structure critical for generating the EPE signal. Together, our results reveal for the first time the functional architecture of EPE-encoding DA neurons crucial for driving fear extinction learning.
Cell-type-specific responses to fungal infection in plants revealed by single-cell transcriptomics
Authors: Bozeng Tang, Li Feng, Michelle T. Hulin, Pingtao Ding, Wenbo Ma
Journal: Cell Host & Microbe (2023)

Pathogen infection is a dynamic process. Here, we employ single-cell transcriptomics to investigate plant response heterogeneity. By generating an Arabidopsis thaliana leaf atlas encompassing 95,040 cells during infection by a fungal pathogen, Colletotrichum higginsianum, we unveil cell-type-specific gene expression, notably an enrichment of intracellular immune receptors in vasculature cells. Trajectory inference identifies cells that had different interactions with the invading fungus. This analysis divulges transcriptional reprogramming of abscisic acid signaling specifically occurring in guard cells, which is consistent with a stomatal closure dependent on direct contact with the fungus. Furthermore, we investigate the transcriptional plasticity of genes involved in glucosinolate biosynthesis in cells at the fungal infection sites, emphasizing the contribution of the epidermis-expressed MYB122 to disease resistance. This work underscores spatially dynamic, cell-type-specific plant responses to a fungal pathogen and provides a valuable resource that supports in-depth investigations of plant-pathogen interactions.
The Index of Severity for Eosinophilic Esophagitis (I-SEE) Reflects Longitudinal Clinicopathologic Changes in Children
Authors: Andrew Dickerson, Ayse Kolemen, Keeler Kime, Kira Chaiboonma, Ranjan Dohil, Glenn T. Furuta, Evan S. Dellon, Seema S. Aceves
Journal: Clinical Gastroenterology and Hepatology (2023)
Non-Gastrointestinal Complications and Short-Term Outcomes in Patients With Anastomotic Leak After Colon Resection: A Propensity Matched Analysis of American College of Surgeons National Surgical Quality Improvement Program Database
Authors: Amir Humza Sohail, Amanda Beneat, Amir Humza Sohail, Andrew Morel, Hassam Ali, Hazim Hakmi, Jennifer Whittington, Manesh Kumar Gangwani, Shahidul Islam, Soban Maan, Tulio Brasileiro Silva Pacheco
Journal: International Journal of Surgery (2023)

Introduction: Anastomotic leak is a devastating complication after colorectal surgery. There is paucity of data on non-gastrointestinal complications after anastomotic leak in this population. We aimed to investigate non-gastrointestinal complications, as well as causes of major morbidity and mortality following anastomotic leak after colorectal resection and hypothesized that non-gastrointestinal complications after anastomotic leak are a sizable proportion of the overall morbidity and mortality in this population. Methods: We used the ACS NSQIP database, and searched for CPT codes for colorectal procedures with primary anastomosis between 2015-2019. The cohorts (anastomotic leak vs. no-leak) were aligned using propensity score matching, and 30-day mortality, length of stay, and readmission outcomes were compared. Results: We identified 4881 patients with anastomotic leak and 150331 patients with no-leak. The overall leak rate was 3.14%. Anastomotic leak group had an 85% longer length-of-stay. Predicted mean (95% CI) length-of-stay for the leak group was 10.2 (9.9-10.5) days vs. 5.5 (5.4-5.7) days for the no-leak group. Anastomotic leak was associated with a higher 30-day risk of unplanned return to the operating room (OR 34.5; 95% CI 27.2-43.8), and thirty-day mortality (OR 2.8; 95% 2.2-3.5). Anastomotic leak was associated with a higher incidence of pulmonary complications including: pneumonia (OR 4.4; 95% CI 3.5-5.6), unplanned intubation (OR 6.3; 95% CI 4.8-8.3), mechanical ventilation (OR 6.3; 95% CI 5.1-8.0), and pulmonary embolism (OR 4.3; 95% CI 2.6-7.0); cardiac complications, including myocardial infarction (OR 2.9 (95% CI 2.0-4.2) and cardiac arrest (OR 3.2; 95% CI 2.1-4.9); and new-onset renal failure requiring dialysis (OR 3.8; 95% CI 2.6-5.5). There was no significant difference in risk of acute kidney injury (OR 1.1; 95% CI 0.6-2.0), and stroke (OR 1.8; 95% CI 0.9-3.6). Conclusion: Colorectal anastomotic leak independently lengthens length-of-stay, and is associated with increased mortality (2.7% vs. 7.2%) after colorectal surgery with an enteric anastomosis.
Engineered mesenchymal stem cell-derived extracellular vesicles constitute a versatile platform for targeted drug delivery
Authors: Wanrong Meng, Linlin Wang, Xueyu Du, Mingzhe Xie, Fan Yang, Fei Li, Zhanxuan E. Wu, Jianguo Gan, Hongxuan Wei, Chang Cao, Shun Lu, Bangrong Cao, Longjiang Li, Ling Li, Guiquan Zhu
Journal: Journal of Controlled Release (2023)
Antimicrobial effect of platelet‐rich fibrin: A systematic review of in vitro evidence‐based studies
Authors: Vittorio Moraschini, Richard J. Miron, Carlos Fernando de Almeida Barros Mourão, Rafael Seabra Louro, Anton Sculean, Luiz Afonso Morgenstern da Fonseca, Monica Diuana Calasans Maia, Jamil Awad Shibli
Journal: Periodontology 2000 (2023)

Abstract This systematic review (SR) aimed to evaluate the antimicrobial potential of different types of platelet‐rich fibrin (PRF) often used in regenerative treatments. An electronic search was performed in four databases and in Gray literature for articles published until January, 2023. The eligibility criteria comprised in vitro studies that evaluated the antimicrobial effect of different types of PRF. For the analysis of the risk of bias within studies, the modified OHAT (Office of Health Assessment and Translation) tool was used. For the evaluation of the results, a qualitative critical analysis was carried out in the synthesis of the results of the primary studies. Sixteen studies published between 2013 and 2021 were included in this SR. The antimicrobial effects of PRF variations (PRF, injectable PRF [I‐PRF], PRF with silver nanoparticles [agNP‐PRF], and horizontal PRF [H‐PRF]), were analyzed against 16 types of bacteria from the oral, periodontal, and endodontic environments. All types of PRF showed significant antimicrobial action, with the antibacterial efficacy being more expressive than the fungal one. The I‐PRF, H‐PRF, and agNP‐PRF subtypes improve antimicrobial activity. According to the OHAT analysis, no study was classified as having a high risk of bias. Evidence suggests that PRF variations have significant antimicrobial activity, with bacterial action being greater than fungal. Evolutions such as I‐PRF, H‐PRF, and agNP‐PRF improve antimicrobial activity. Future studies analyzing the clinical effect of these platelets are fundamental. This SR was registered in INPLASY under number INPLASY202340016.